Computational identification of lineage-committed precursors in mammalian organogenesis reveals a novel hematopoietic enhancer regulating Bhlhe41 expression

Abstract Lineage-committed precursors are essential yet rarely identified in mammalian organogenesis, as they lack definitive molecular signatures required for conventional marker-based approaches. Herein, we developed iCommitted, an integrated multi-omics computational pipeline for precise identification of these precursors. iCommitted first reconstructs in vivo organogenesis by modeling the in vitro differentiation trajectory spanning naïve to terminally differentiated cells. It then integrates epigenomic (ATAC-seq/DNase-seq) and transcriptomic (RNA-seq) data to achieve standardized developmental staging and precursor identification. Applied to mammalian hematopoiesis, iCommitted robustly identified hematopoietic progenitors as the hematopoietic lineage-committed precursors. Subsequent cis-regulatory annotation generated a high-confidence atlas of 16 774 hematopoietic cis-regulatory elements. Functional analysis of the atlas further pinpointed a 218-bp hematopoietic enhancer (chr6:145 855 899-145 856 116) that regulates Bhlhe41 expression during lineage commitment. This study establishes a valuable approach for identifying lineage-committed precursors and elucidating regulatory mechanisms in mammalian organogenesis, offering broad utility in developmental biology.